Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of E. coli in the presence and absence of ethanol

ABSTRACT: We measured transcriptional changes in an effort to understand mechanisms of action resulting from the introduction of global transcriptional machinery engineering in E. coli in the presence and absence of ethanol. Experiment Overall Design: We explored two types of experimental factors: genetic variation (mutated transcriptional machinery) and environmental variation (ethanol concentration).

ORGANISM(S): Escherichia coli

SUBMITTER: Joel Moxley

PROVIDER: E-GEOD-3665 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global transcription machinery engineering: a new approach for improving cellular phenotype.

Alper Hal H Stephanopoulos Gregory G

Metabolic engineering 20070108 3

It is now generally accepted that most cellular phenotypes are affected by many genes. As a result, engineering a desired phenotype would be facilitated enormously by simultaneous multiple gene modification, yet the capacity to introduce such modifications is very limited. Here, we demonstrate that the components of global cellular transcription machinery (specifically, sigma(70)) can be engineered to allow for global perturbations of the transcriptome, which can help unlock complex phenotypes. ...[more]

PMID: 17292651

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Project description:Desulfovibrio vulgaris has been studied extensively for its potential in the bioremediation of heavy metals and radionuclides. Hydrocarbons and solvents, as frequent environmental co-contaminants, have been reported to inhibit microbial activities and thereby pose a limitation on bioremediation efficiency. As a part of the Genomes: GTL project to deduce the stress response pathways in metal/radionuclide reducing bacteria, we studied the responses of D. vulgaris to ethanol, which is a solvent and co-contaminant frequently encountered at contaminated DOE sites. Growth experiments in closed vessels at 37 °C indicated that D. vulgaris could maintain normal growth with 1%(v/v) ethanol. The growth rates were reduced with increasing ethanol concentrations at 2% and 5%. Growth ceased when ethanol concentration was raised to 5%(v/v). Cell lysis was apparent with decreasing optical density following 10% ethanol addition. To assess the mechanism of ethanol inhibition, genome-wide transcriptional profiles were analyzed from D. vulgaris cultures following ethanol (5% v/v) treatment using whole-genome microarrays. The ethanol treatment altered the expression of a large number of genes in the D. vulgaris genome, of which 354 were up-regulated greater than 2 fold and 217 were down-regulated by over 2 fold. As expected, changes in the transcriptional profile were similar to those of the stress response to acetone, which is also a solvent. Transcripts highly up-regulated included genes encoding the flagella structural subunits, suggesting motility as a mechanism of solvent stress response. Another group of genes highly induced were chaperones, such as dnaJ, groES, and hsp20, indicating the importance of maintaining proper protein folding under ethanol stress. Down-regulated genes included two groups of genes, ribosomal proteins and amino acid transporters, consistent with the growth inhibition by ethanol observed in growth studies. These results were interpreted that D. vulgaris responds to elevated solvent levels by increased motility and maintenance of proper protein functions. Current work is focused on the analysis of regulatory pathways based on temporal transcriptional dynamics. Keywords: Stress response

Dataset Information

Transcription profiling of E. coli in the presence and absence of ethanol

Publications

Global transcription machinery engineering: a new approach for improving cellular phenotype.

Similar Datasets

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